+Open data
-Basic information
Entry | Database: PDB / ID: 7ow2 | ||||||
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Title | E3 RING ligase binding domain with peptide | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / ubiquitin ligase | ||||||
Function / homology | Function and homology information antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | James, L.C. | ||||||
Citation | Journal: To Be Published Title: E3 ligase targeting domain Authors: James, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ow2.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ow2.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ow2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7ow2 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7ow2 | HTTPS FTP |
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-Related structure data
Related structure data | 7ovxC 2iwgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19303.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli (E. coli) References: UniProt: Q9C029, RING-type E3 ubiquitin transferase #2: Protein/peptide | Mass: 760.943 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF187 / Production host: Homo sapiens (human) / References: RING-type E3 ubiquitin transferase #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.54 % |
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Crystal grow | Temperature: 297 K / Method: batch mode / pH: 6.7 / Details: 23% PEG 6K, 0.1 M NaCl, 50mM HEPES pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å |
Detector | Type: OXFORD TITAN CCD / Detector: CCD / Date: Nov 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→93.64 Å / Num. obs: 47982 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.29 Å / Num. unique obs: 1398 / CC1/2: 0.963 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IWG Resolution: 2.17→93.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.246 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.45 Å2 / Biso mean: 40.283 Å2 / Biso min: 21.72 Å2
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Refinement step | Cycle: final / Resolution: 2.17→93.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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